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- PDB-6pmp: Crystal structure of a fragment of rat phospholipase Cepsilon EF3-RA1 -

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Basic information

Entry
Database: PDB / ID: 6pmp
TitleCrystal structure of a fragment of rat phospholipase Cepsilon EF3-RA1
Components1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
KeywordsSIGNALING PROTEIN / phospholipase / lipase / TIM barrel / Ras-association domain
Function / homology
Function and homology information


Synthesis of IP3 and IP4 in the cytosol / : / regulation of Ras protein signal transduction / phosphoinositide phospholipase C / diacylglycerol biosynthetic process / phosphatidylinositol phospholipase C activity / regulation of G protein-coupled receptor signaling pathway / phospholipase C activity / glomerulus development / phosphatidylinositol-mediated signaling ...Synthesis of IP3 and IP4 in the cytosol / : / regulation of Ras protein signal transduction / phosphoinositide phospholipase C / diacylglycerol biosynthetic process / phosphatidylinositol phospholipase C activity / regulation of G protein-coupled receptor signaling pathway / phospholipase C activity / glomerulus development / phosphatidylinositol-mediated signaling / regulation of protein kinase activity / lipid catabolic process / positive regulation of lamellipodium assembly / guanyl-nucleotide exchange factor activity / epidermal growth factor receptor signaling pathway / small GTPase binding / lamellipodium / phospholipase C-activating G protein-coupled receptor signaling pathway / Ras protein signal transduction / G protein-coupled receptor signaling pathway / Golgi membrane / enzyme binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / Ras association (RalGDS/AF-6) domain / Phosphatidylinositol-specific phospholipase X-box domain profile. / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / Ras association (RalGDS/AF-6) domain / Phosphatidylinositol-specific phospholipase X-box domain profile. / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / EF-hand domain pair / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsRugema, N.Y. / Lyon, A.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)1R01HL141076-01 United States
American Heart Association16SDG29930017 United States
American Cancer SocietyIRG-14-190-56 United States
CitationJournal: Commun Biol / Year: 2020
Title: Structure of phospholipase C epsilon reveals an integrated RA1 domain and previously unidentified regulatory elements.
Authors: Rugema, N.Y. / Garland-Kuntz, E.E. / Sieng, M. / Muralidharan, K. / Van Camp, M.M. / O'Neill, H. / Mbongo, W. / Selvia, A.F. / Marti, A.T. / Everly, A. / McKenzie, E. / Lyon, A.M.
History
DepositionJul 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
B: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
C: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
D: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)370,4398
Polymers370,2794
Non-polymers1604
Water1,20767
1
A: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6102
Polymers92,5701
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6102
Polymers92,5701
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6102
Polymers92,5701
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6102
Polymers92,5701
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.572, 127.755, 139.337
Angle α, β, γ (deg.)90.00, 101.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA1303 - 209123 - 811
21GLNGLNBB1303 - 209123 - 811
12PROPROAA1303 - 209023 - 810
22PROPROCC1303 - 209023 - 810
13LYSLYSAA1303 - 208923 - 809
23LYSLYSDD1303 - 208923 - 809
14PROPROBB1303 - 209023 - 810
24PROPROCC1303 - 209023 - 810
15LEULEUBB1303 - 208823 - 808
25LEULEUDD1303 - 208823 - 808
16LYSLYSCC1303 - 208923 - 809
26LYSLYSDD1303 - 208923 - 809

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 / Phosphoinositide phospholipase C-epsilon-1 / Phospholipase C-epsilon-1 / PLC-epsilon-1


Mass: 92569.664 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Plce1, Plce / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q99P84, phosphoinositide phospholipase C
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop / Details: 6.25% PEG 4000, 100 mM MES pH 6.00, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.73→136.72 Å / Num. obs: 84933 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.971 / Rmerge(I) obs: 0.268 / Rpim(I) all: 0.171 / Rrim(I) all: 0.319 / Net I/σ(I): 5.1 / Num. measured all: 288747 / Scaling rejects: 500
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.73-2.883.51.79443223123590.3341.1222.121.199.7
8.64-136.723.30.049919427830.9960.0310.05814.999.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OHM

3ohm
PDB Unreleased entry


Resolution: 2.73→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.9 / SU B: 51.094 / SU ML: 0.42 / Cross valid method: THROUGHOUT / ESU R: 2.22 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27278 4196 5 %RANDOM
Rwork0.23397 ---
obs0.23591 80469 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.286 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å2-0.12 Å2
2---0.21 Å20 Å2
3---0.79 Å2
Refinement stepCycle: 1 / Resolution: 2.73→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19622 0 4 67 19693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01320066
X-RAY DIFFRACTIONr_bond_other_d0.0040.01718612
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.64227127
X-RAY DIFFRACTIONr_angle_other_deg1.2531.57143386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.84352415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78922.8121067
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.656153579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.92815115
X-RAY DIFFRACTIONr_chiral_restr0.0730.22599
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0222053
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024080
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1571.3469741
X-RAY DIFFRACTIONr_mcbond_other1.1571.3459740
X-RAY DIFFRACTIONr_mcangle_it2.0072.00512129
X-RAY DIFFRACTIONr_mcangle_other2.0072.00512130
X-RAY DIFFRACTIONr_scbond_it1.0731.46410325
X-RAY DIFFRACTIONr_scbond_other1.0731.46410326
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8672.1414999
X-RAY DIFFRACTIONr_long_range_B_refined3.32914.57920707
X-RAY DIFFRACTIONr_long_range_B_other3.32914.58520703
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A190090.07
12B190090.07
21A187690.08
22C187690.08
31A188600.07
32D188600.07
41B188760.07
42C188760.07
51B188390.07
52D188390.07
61C187490.07
62D187490.07
LS refinement shellResolution: 2.732→2.802 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 290 -
Rwork0.327 5829 -
obs--99.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.92080.5830.762.3852-0.07654.4856-0.0558-0.3221-0.02150.141-0.04080.4282-0.2548-0.66510.09660.3620.0860.14540.42740.0370.893519.798-33.50522.119
20.44750.3974-0.32271.6989-0.43180.3997-0.0542-0.0225-0.02520.0640.0131-0.1376-0.01090.09480.0410.0727-0.00330.06990.3064-0.02261.024544.05-16.094.024
34.1552.3777-3.57452.59610.09676.9738-0.2097-0.165-0.1994-0.0633-0.141-0.14680.57170.12290.35070.4760.10690.11650.47140.031.03669.85618.56-14.498
40000000000000000.6362000.636200.6362000
56.08860.43090.47790.6933-0.41185.3404-0.0273-0.29730.06570.2961-0.0835-0.37610.19390.68450.11090.3769-0.01560.01430.41-0.00490.88724.596-4.40224.028
61.30780.69480.30072.00410.45330.2773-0.0232-0.0013-0.1386-0.06070.04020.1165-0.0546-0.1207-0.0170.0319-0.02580.070.34250.04041.04541.027-22.193-3.956
76.52580.16287.10170.00680.18447.7699-0.4421-0.15720.3704-0.04370.00840.0322-0.6478-0.21740.43370.72960.07540.06010.2721-0.10421.0883-20.836-55.714-18.122
81.7040.2709-0.3270.58671.28344.44490.1331-0.328-0.0410.3-0.08270.15090.2247-0.4503-0.05040.4389-0.0220.18820.49450.0390.98183.829-9.1933.536
94.5116-0.95560.40572.41841.21655.34660.0822-0.41720.24650.2725-0.32450.6523-0.0507-0.70360.24230.31610.01250.21790.4903-0.04121.12397.99-28.26192.471
101.17460.6262-0.37861.594-0.49030.4341-0.0386-0.12360.0957-0.0593-0.0127-0.08990.05190.08730.05130.009-0.00980.05150.3716-0.02851.134432.145-9.91864.986
110.14330.12010.08561.0780.97520.92070.19-0.1165-0.1261-0.1805-0.4278-0.0456-0.1655-0.40640.23780.3244-0.02750.04350.22560.01711.701445.2955.17245.713
121.15210.987-0.39880.97590.02075.37290.2292-0.31950.09520.4235-0.20460.00240.32910.8931-0.02460.44260.04940.03650.5690.06891.07728.23-22.981100.736
135.92870.40550.52053.35261.0765.9099-0.0313-0.66980.21490.0405-0.1627-0.750.32260.47980.1940.29280.0990.0210.56680.08161.126412.8310.49490.302
140.82860.61950.34112.230.1470.1757-0.01-0.0096-0.0237-0.02010.0440.1438-0.0185-0.0849-0.03410.0407-0.02440.08220.34990.01691.1197-11.573-19.66465.775
155.33811.22413.94351.9877-1.59876.6387-0.2634-0.0360.2794-0.00340.14760.1333-0.4335-0.34370.11580.53960.08280.05730.5131-0.02141.1084-35.879-51.41454.019
163.491.56361.63070.76560.38622.63670.535-1.2310.1120.2423-0.54360.08070.2944-0.74280.00860.2559-0.08960.18740.9185-0.04671.1201-7.13-2.60299.906
170.0861-0.0483-0.15270.083-0.0290.51040.0183-0.0245-0.0135-0.00910.0270.023-0.04150.0462-0.04530.095-0.03730.03520.26750.0120.86222.529-11.70531.557
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1303 - 1360
2X-RAY DIFFRACTION2A1361 - 1523
3X-RAY DIFFRACTION2A1637 - 2100
4X-RAY DIFFRACTION3A1524 - 1636
5X-RAY DIFFRACTION4A1985 - 2096
6X-RAY DIFFRACTION5B1303 - 1360
7X-RAY DIFFRACTION6B1361 - 1523
8X-RAY DIFFRACTION6B1637 - 1984
9X-RAY DIFFRACTION7B1524 - 1636
10X-RAY DIFFRACTION8B1985 - 2100
11X-RAY DIFFRACTION9C1303 - 1360
12X-RAY DIFFRACTION10C1361 - 1523
13X-RAY DIFFRACTION10C1637 - 1984
14X-RAY DIFFRACTION11C1524 - 1636
15X-RAY DIFFRACTION12C1985 - 2100
16X-RAY DIFFRACTION13D1303 - 1360
17X-RAY DIFFRACTION14D1361 - 1523
18X-RAY DIFFRACTION14D1637 - 1984
19X-RAY DIFFRACTION15D1524 - 1636
20X-RAY DIFFRACTION16D1985 - 2100
21X-RAY DIFFRACTION17F1 - 93

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